[gmx-users] simulation single molecule in water
Emanuel.Birru at monash.edu
Tue May 7 09:40:02 CEST 2013
It would be better if you run it a bit longer than 10ns and check the density again. But it is not a big problem I guess as the density of water at 300K should not be exactly 1000kg/m^3. Its ~1000kg/m^3 at 277K. do not expect to get exactly real value :) Additionally your system is not purely water molecules in a box there is a small molecule in it which might have an effect on the density.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Souilem Safa
Sent: Tuesday, 7 May 2013 4:38 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] simulation single molecule in water
Dear gromacs users,
I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size.
I got the toplogy of my molecule via PRODRG.
After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\N) ,actually I got around 950.
I have checked my mdp file in the NPT step and I was wondering about tau_p that I should use. First I used 2.0 ps with Parrinello-Rahman coupling.
After checking in gromacs archive, I found it is better to use 0.5 ps, I have changed tau-p ,but I still have density value less than 1000.
Details of my mdp file are below :
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10000 ps, 1 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
coulombtype = PME ; Particle Mesh Ewald for long-range
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = system ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 0.50 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
What should be the origin of this density difference?
looking forward to your advise
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